The Control Panel is the first window to be displayed when NMRView starts up, and consists of a single menubar. Note that on Mac OS X the menubar will generally be displayed not as a separate window, but on the Desktops screen menu bar. The menus available through the menubar may be used to bring up various other NMRView windows. The options available through each menu item are summarized below.
Create a new project. You will be presented with a file browser to use in specifying the location and name of the new project. The project will be created as a new folder with appropriate sub-folders.
Open an existing project. You will be presented with a file browser to use in selecting the existing project.
A menu displaying recently used projects (up to 20). Selecting a project name from the menu will open that project.
Save the current project (including STAR3 file and open windows).
Save the current data as a new project. (including STAR3 file and open windows).
Display a list of saved states of the current project. Selecting an item from the list and clicking Open will reload the project as contained in that saved state.
Display the project attributes browser used to manage NMRVIEW projects. Use the attributes browser to set attributes like locations of dataset folders.
Close the current project. This removes all open information such as datasets, peak lists, and molecular structures.
Brings up a file selection panel for reading a BMRB Star file (NMRView database file). Almost any kind of analysis that NMRView can perform can be stored in a Star file.
Save STAR3 As...
Brings up a file selection panel for writing a BMRB Star File.
Save STAR3 (Auto Increment)
Saves a BMRB STAR file using a name automatically generated from the last saved STAR file. For example, if the last file saved was "myproject_3.str" the new file will be "myproject_4.str". This is a convenient way to make frequent updates of your data to a STAR file as you work on a project. To have this work properly you should start with an initial file name that ends with a non-integer character followed by an integer value (as in the above example).
Fetch From BMRB...
Load the set of files found in your last session. Each time you use Scan Directory (or Clear and Scan Directory) the files found will be stored in a file. The files in this table will be opened.
Earlier versions (before 8.0) of NMRViewJ used the STAR 2 file format. If you need to work with these older files use the choices in this menu. But some features of NMRViewJ (especially relating to RunAbout) can only be saved in STAR 3 files, so its a good idea to switch to the newer format. You can open a file in STAR 2 format, and save it out in STAR 3 format.
Read STAR2 File
Use a File Browser to Open and read a STAR (version 2.x) File
Write STAR2 File
Use a File Browser to Save a STAR (version 2.x) File.
Select Prefs to open up the Preferences Panel. This can be used to set various user preferences for NMRView. On Mac OS X this menu item will be found under the NMRVIEW menu
Print the active spectrum.
Show the NMRView console. The console can be used for command line input and displays the output of various commands. The NMRView console is based on the tkCon console developed by J. Hobbs.
Quit the NMRVIEW program.
Select this to open a File Selection Panel that can be used to select datasets to be opened.
Select this to open a File Selection Panel that can be used to select datasets to be opened. When the dataset is opened a window will be created and the dataset will be drawn
Select this to open a window containing a table of all currently opened datasets. The use of this table is described in the chapter on Datasets.
When you quit from NMRViewJ the file paths for currently opened datasets are stored into a preferences area containing recently opened datasets. Selecting this menu item will load these recently opened datasets.
Varian phase files are stored as serial files (see Datasets chapter) and thus are less efficiently accessed than NMRView format files. Select this menu entry to get a file selection dialog to select a Varian phase file that can then be converted into an NMRView format file. The phase file must exist in the normal Varian directory hierarchy so that the procpar file can be read as well.
Select this to open a Datasets Manage Panel that can be used to reference or close datasets.
Select this to combine a set of selected 2D datasets into a single 3D dataset where each 2D dataset is on a plane. Choosing this menu item will display a file browser you can use to select the datasets with. After selecting datasets you'll be prompted for the name of the 3D dataset to create.
Select this to pick peaks in all currently opened datasets. As with the similar operation available from the Datasets table this is only useful if the datasets have reasonable default contour levels (or if a reasonable value can be automatically determined from the datasets signal to noise level).
Select this to copy an image of the current spectrum window to the clipboard from where it can be pasted into another application
Display an interface in which you can set up synchronization of the view between various specified spectral display windows.
Export a graphics file rendering of the current spectrum. You will be prompted for the file name and type of graphics file. Current formats include vector formats such as EPS, PDF and SVG and bitmap formats such as GIF, JPEG and PNG
Select this to open a File Selection Panel that can be used to select datasets to be opened. When the dataset is opened a window will be created and the dataset will be drawn.
Open a window that will display the current chemical shift positions of the two crosshairs in the active window. If the window is displaying a dataset with three or four dimensions then the chemical shift ranges of the displayed planes will also be displayed. The row labeled "D:" in the monitor window will display the chemical shift difference between the two crosshairs for the x and y dimensions, and the difference between the top and bottom displayed plans for z and z2.
Select this to open a Windows Management Panel that can be used to raise spectrum windows to the front of the display or to delete them.
Display the graphical interface for displaying the bindings that relate key presses in a spectrum window to actions that occur.
Select this to open display a dialog from which you can create a series of strips of spectra, as documented in the "Strips" chapter.
Select this to save the area of the dataset between the crosshair cursors into a new smaller dataset. You'll be prompted with a file dialog to choose the file name and after saving asked if you want to open up the new smaller dataset.
Display a list of currently saved spectral views (favorites). Only active if a project is open.
Display a graphical interface used for jumping around to various positions in spectra.
Hide all windows with spectra.
Show all windows with spectra.
In premium mode, spectra can be displayed in windows that can include not only spectra, but also a wide variety of graphical objects such as rectangles, text, and lines. Canvases can also include various charts, including xy and bar charts.
Save a NMRViewJ/dataChord format canvas file. This will save all the graphic items on a single canvas (which may include multiple spectra).
Open a NMRViewJ/dataChord format canvas file. This will create a new toplevel window containing all the graphic items in the saved file. Spectrum items in the graphic file may depend for their display on the datasets used in originally drawing them. The software will check if the dataset are already opened, attempt to open them from locations specified in the graphics file or in your current project directories. If they can't be found you will be prompted with a file browser to explicitly open them.
Display a browser to let you browse through saved canvas files.
Export (Bitmap Image)...
Export a graphics file rendering of the current spectrum in a bitmap format such as PNG, GIF, or JPG.. You will be prompted for the file name. The file format will be determined from the extension of the file name.
Export (Vector Graphics)...
Export a graphics file rendering of the current spectrum. You will be prompted for the file name and type of graphics file. Current formats include vector formats such as EPS, PDF and SVG and bitmap formats such as GIF, JPEG and PNG. This menu item will let you select both vector formats and bitmap formats, but it is preferable to use the previous menu item for bitmap formats.
Create a new toplevel canvas window with a spectrum item in it and the spectrum control iconbar across the top.
Create a new toplevel canvas window with a multiple spectra in it and the spectrum control iconbar across the top. You will be prompted for the total number of spectra and the number of rows in the display grid.
Create a new toplevel canvas window without any content (or iconbar).
Insert a new spectrum item onto the canvas.
Insert a new rectangle item onto the canvas.
Insert a simple text item onto the canvas. You can change the font and color of simple text items, but don't have control over individual characters or more complicated attributes.
Insert a new formatted text item onto the canvas. Formatted items can have most any attributes (font, superscript, bold, italics, etc.) changed and special symbols added.
Insert a new annotation item onto the canvas. Annotation items are a line with a simple text string at one end and an arrow head at the other.
Insert a new table item onto the canvas. Table items are text formatted as a table.
Insert a new line item onto the canvas.
Insert a new arc item onto the canvas.
Insert a new oval item onto the canvas.
Insert a new xy plot onto the canvas.
Insert a new bar plot onto the canvas.
Insert a new statistical bar plot item onto the canvas.
Remove the currently selected item(s) from the canvas. Cut items will placed on the clipboard so they can be pasted elsewhere.
Copy the currently selected item(s) onto the clipboard.
Paste items on the clipboard into the current canvas. Items can be items that were cut or copied from a canvas, or various other item types copied from other programs including text and images.
Send to Back
Send the currently selected item to be below all other canvas items.
Send the currently selected item to be below the next lowest (in display order) item in the canvas.
Send the currently selected item to be above all other canvas items.
Bring to Front
Send the currently selected item to be in front of the next highest (in display order) item in the canvas.
Group together currently selected items. Grouped items will be moved together when they are dragged around the canvas with the mouse.
UnGroup the currently selected items.
Lock the currently selected items. Locked items can't be moved or resized. The selection handles of locked items will contain an "x" symbol.
Unlock the currently selected items.
Distribute all spectra in the canvas so they are evenly distributed in a row across the canvas.
Distribute all spectra in the canvas so they are evenly distributed in a column down the canvas.
Distribute all spectra in the canvas so they are displayed as a grid with a number of rows and columns that can accommodate all the spectra.
Adjust the display of axes and border sizes for efficient use of space in gridded windows. Only axes along the left and bottom sides of the canvas will be shown. This is the default when gridded windows are first created.
Adjust the display of axes and border sizes so that the left vertical and bottom horizontal axes are shown for all windows.
Open and setup the strip control dialog for the current canvas spectrum.
Arrange all spectra so they are in a reasonable layout based on type (for example, HSQC occupying most space, with proton across top and carbon across side).
Display the Graphical Inspector that can be used to view and change the attributes (colors, fonts, sizes etc.) of items on the canvas.
Select this to bring up Peak Analysis Panel that can be used to display and edit information about peaks, including their assignment value, chemical shift positions, widths and intensities.
More than one peak inspector can be displayed. This will create a new one.
Whereas the Peak Analysis Panel displays information about one peak at a time the Peak Table displays a table of information about every peak in a selected peak list. The table can be sorted and groups of peaks marked for deletion.
More than one peak table can be displayed. This will create a new one.
Show a table of all the open peak lists. This will include a row for each peak list with the peak list name, the dataset (if any) assigned to that peak list, the number of peaks in the peak list, the number of deleted peaks, the number of peaks with full assignments, the number of peaks with partial assignments, and the number of unassigned peaks.
Write the peak list displayed in the current peak inspector to a text file (.xpk).
Write Aria XML List
Write the peak list displayed in the current peak inspector to a text file in the XML format used by ARIA.
Read an NMRVIEW format (.xpk) file in.
Make New List
Create a new empty peak list. You will be prompted for the names for the dimensions the list will have. This command is for various advanced uses.
Read All Lists
Read all the peak list files (.xpk) in the current working directory.
Write All Lists
Write all the current peak lists to NMRVIEW format (.xpk) files.
Read Sparky Save File
Read in a text file created with the Sparky save command. A new peak list with the contents of the file will be created.
Remove peaks that have been marked for deletion. This is not reversible, and will create gaps in the peak numbering.
Renumber peaks (after compressing the list) so that there are no gaps in the peak numbering.
Compress and Degap
Combination of compress, followed by degap. Peaks will be permanently deleted, and the list will be sequentially numbered with no gaps.
Delete the current list displayed in the peak inspector.
Display a graphical interface for setting various attributes of the current peak list.
Display a graphical interface that can be used to collapse multiple peaks separated by defined splittings into a single centered peak.
Cluster peaks in the current list based on their chemical shifts in certain dimensions. Dimensions used and the tolerance that determines whether peaks are clustered are set with a peak template. Peak dimensions that are clustered will have a common resonance id after clustering.
Not yet active.
Search all lists for peaks whose chemical shifts (for matching dimensions) are similar (within the id tolerance) of the shifts of the current peak. Matching peaks are listed to console.
Display the Peak Identification interface. This interface will suggest possible assignments for the current peak based on the chemical shifts of assigned atoms, and distances in the current structures.
Display the Peak Filtering interface. This interface allows you to delete peaks based on various criteria.
Display an interface for measuring HN-HA coupling constants as described in Kuboniwa et al. J. Biomol. NMR 4 (1994), 871-878:
Display an interface for measuring the heteroncuclear NOE using peaks in the current list and two datasets, one with, and one without, the NOE active.
Minimum Chemical Shift
Display an interface for measuring the minimal chemical shift change for each residue in a chemical shift perturbation experiment (typically in the presence of a ligand).
Peak Peak Matching
Display an interface for coming up with the optimal matching of peaks in two different lists.
Atom Peak Matching
Display an interface for coming up with the optimal matching of peaks in one list with the chemical shift assignments of the current molecule.
Each peak list can have a set of patterns (like i.hn, i-1.c etc.) for the types of atoms that give rise to the peaks. This command displays an interface used to check the consistency of a peak lists assignments with its patterns.
Check the assignments of a selected peak list with expected values for the assigned atom types (based on BMRB statistics).
Display an interface used to search peak lists for peaks based on various criteria.
Each peak list has an associated dataset. By default this dataset is the one from which the list was originally picked. You can use this command to select a dataset to be assigned to a list.
For each peak in the list, integrate the intensities over the "footprint" of the peak in the dataset associated with this list.
For each peak in the list, integrate the intensities over the optimal elliptical "footprint" of the peak in the dataset associated with this list.
For each peak in the list get the intensity at the peak center from the dataset associated with this list.
Plot Vol. vs. Intensities
Plot an XY chart with the one symbol for each peak positioned on the X axis at the peaks intensity, and the Y axis at the peaks volume.
Sort the peaks by their intensities and plot the peak intensities in decreasing order.
Sort the peaks by their volumes and plot the peak volumes in decreasing order.
Select this to bring up the Assignments Panel that is used to keep track of chemical shift assignments.
Add a peak at the position of the black crosshair.
Select this to bring up a sequence display panel to display the residue sequence of the molecule.
Select this to bring up a panel for creating and editing NOE restraint lists.
Display a table for identifying NOES, and generating and analyzing distance constraints.
Display a table for generating and analyzing angular constraints.
Select this to open up the RunAbout tool used for assigning proteins using triple resonance NMR experiments.
Select this to bring up a panel for analyzing time-dependent properties (e.g., relaxation).
Select this to bring up a titration panel for analyzing titration data.
IPAP is a set of experiments and an analysis protocol for measuring dipolar coupling constants in partially oriented media.
Distribute all spectra in the canvas so they are evenly distributed in a row across the canvas.
Bring up a file selection dialog to select and open a file containing an amino acid, DNA, or RNA sequence. See the section on Molecular Structures to learn about the format of this file.
PDB File (using library)
Bring up a file selection dialog to select and open a PDB format file. This is the standard way to read in pdb files. NMRView first reads the pdb file to determine the amino acid sequence. Next, it reads the corresponding residues from the residue library. Finally, it reads coordinates from the pdb file for those atoms that have names matching the names in the residue library. Atoms, that do not have a match in the residue library will not be entered into the structure list. Atoms that are in the residue library but not in pdb file, will be included in structure list but will not be displayed. See the section on Molecular Structures to learn about using molecular structures in NMRView.
Reads a file of atomic coordinates of a macromolecule. File must be stored in the PDB format as defined by the Protein Data Bank (now the RCSB). This command does not also read from the residue library so no connectivity information is available. If this is needed use the pdb command instead.
Ligand File (.mol, .sdf)
Open a small molecule (.mol or .sd) file and add it to the current molecular topology.
Write ARIA XML Molecule
Write a text file representation of the current molecule in the ARIA XML format.
Analyze the names of the atoms in the current molecule to determine if you are using the IUPAC or XPLOR style of nomenclature. A selection of atoms violating the most-likely nomenclature will be listed.
Offset the residue numbering (and any assigned peaks) by a specified number.
Bring up a file selection dialog to select and open a PDB format file. Reads the PDB file filename and attempts to match the atoms to atoms in the structure in memory. If atoms match by residue name, atom name, sequence number, chain id, and alternate identifier then the coordinates corresponding to each atom matched are assigned the value of the coordinates of that atom in file.
PDB File (multiple files)...
Reads in coordinates from a series of PDB files. All PDB files in the directory are read that whose name ends in an integer value (like file1.pdb, file03.pdb, file41.pdb etc.). Each coordinate set is stored a separate structure identified by the integer number in the file name. The command only reads in the coordinates, the topology must have been read in previously.
PDB File (representative)...
Reads in coordinates from a single file and stores it in structure 0. Information about the structure is stored in the STAR Saveframe for a representative structure.
Bring up a file selection dialog to select and open an SD format file (commonly used for "small" molecules)
Display an interface for selecting which structures will be used in other tools like the peak identification and constraint table, and for calculating superpositions and residue rms values.
Display a molecular viewer for visualizing the current structure and constraints(Premium feature).
Display a window showing various details about the currently running instance of NMRVIEW
Display the full manual for NMRVIEW
Display an interface in which you can compose a bug report to be sent via your email program.